Check simulation sim_4.5
Alessio Crippa
12 February, 2019
Dynamic report for checking simulation design (4.5)
True mean Progression Free Time (PFT)
Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
---- 7.11 7.11 13.75 7.11 7.11
---+ 7.11 7.11 13.75 7.11 7.11
--+- 7.11 7.11 13.75 7.11 7.11
--++ 7.11 7.11 13.75 7.11 7.11
-+-- 7.11 7.11 13.75 7.11 7.11
-+-+ 7.11 7.11 13.75 7.11 7.11
-++- 7.11 7.11 13.75 7.11 7.11
-+++ 7.11 7.11 13.75 7.11 7.11
+--- 7.11 7.11 13.75 7.11 7.11
+--+ 7.11 7.11 13.75 7.11 7.11
+-+- 7.11 7.11 13.75 7.11 7.11
+-++ 7.11 7.11 13.75 7.11 7.11
++-- 7.11 7.11 13.75 7.11 7.11
++-+ 7.11 7.11 13.75 7.11 7.11
+++- 7.11 7.11 13.75 7.11 7.11Graduation output
$superiority
Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
all 0 0 1 0 0
TP53- & AR- 0 0 0 0 0
TP53+ 0 0 1 0 0
DRD+ 0 0 0 0 0
TEfus+ 0 0 0 0 0
$inferiority
Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
all 0 0 0 0 0
TP53- & AR- 0 0 0 0 0
TP53+ 0 0 0 0 0
DRD+ 0 0 0 0 0
TEfus+ 0 0 0 0 0Final probability of superioriry by signatures and biomarkers subtypes
$p_sign
Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
all 0.65 0.66 0.99 0.53 0.75
TP53- & AR- 0.41 0.46 1.00 0.87 0.69
TP53+ 0.84 0.71 0.94 0.61 0.57
DRD+ 0.55 0.72 0.85 0.72 0.69
TEfus+ 0.64 0.31 0.91 0.57 0.74
$p_type
Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
---- 0.21 0.31 1.00 0.15 0.45
---+ 0.73 0.65 0.93 0.80 0.84
--+- 0.97 0.60 0.93 0.24 0.52
--++ 0.51 0.62 0.97 0.74 0.53
-+-- 0.33 0.34 0.84 0.68 0.45
-+-+ 0.46 0.50 0.66 0.87 0.53
-++- 0.48 0.74 0.64 0.54 0.35
-+++ 0.68 0.53 0.55 0.50 0.51
+--- 0.49 0.71 0.65 0.26 0.46
+--+ 0.34 0.09 0.38 0.17 0.54
+-+- 0.53 0.61 0.60 0.55 0.52
+-++ 0.57 0.25 0.64 0.31 0.54
++-- 0.30 0.70 0.79 0.32 0.71
++-+ 0.47 0.45 0.47 0.40 0.64
+++- 0.73 0.70 0.60 0.76 0.66
Control Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
---- 153 28 59 27 43 43
---+ 19 14 15 4 16 10
--+- 54 54 29 16 12 18
--++ 38 12 19 6 25 15
-+-- 37 1 2 8 8 5
-+-+ 17 4 3 9 12 7
-++- 4 2 6 2 3 3
-+++ 4 3 0 0 1 3
+--- 19 8 15 2 2 7
+--+ 11 7 5 1 5 16
+-+- 3 2 4 0 1 1
+-++ 19 4 5 3 7 10
++-- 5 6 6 2 6 5
++-+ 1 1 0 2 2 3
+++- 5 1 1 1 2 1 Control Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
all 389 147 169 83 145 147
TP53- & AR- 226 47 79 48 79 65
TP53+ 127 78 64 28 51 51
DRD+ 73 18 18 24 34 27
TEfus+ 109 45 47 25 68 64
Number of events, PT, and rate by subtype (over time)
Number of events, PT, and rate by signature (over time)
Analysis of final simulated results
Sample of 10 rows:
id trt trt2 line subtype delta month0 time_m all TP53- & AR- TP53+ DRD+ TEfus+
565 507 Cabazitaxel Cabazitaxel 1 +-++ 1 16 1.1326152 1 0 1 0 1
264 244 Control Docetaxel 1 --+- 1 8 4.6989086 1 0 1 0 0
158 150 Docetaxel Docetaxel 1 +--+ 1 4 12.2078841 1 0 0 0 1
120 113 Carboplatin Carboplatin 1 +++- 1 3 1.6844444 1 0 1 1 0
1005 902 Control Enzalutamide 1 ---- 1 30 0.9303245 1 1 0 0 0
261 241 Control Enzalutamide 1 ---- 1 8 23.1234898 1 1 0 0 0
1006 903 Control Enzalutamide 1 ---- 1 30 2.2252601 1 1 0 0 0
262 242 Control Abiraterone 1 ---- 1 8 5.5241276 1 1 0 0 0
956 866 Cabazitaxel Cabazitaxel 1 -+-+ 1 28 1.0317802 1 1 0 1 1
131 123 Control Abiraterone 1 --+- 1 4 6.9556186 1 0 1 0 0Descriptives
Mean number of progressions and follow-up time:
$all
# A tibble: 6 x 4
trt progressions PT rate
<fct> <dbl> <dbl> <dbl>
1 Control 334 2387. 0.140
2 Enzalutamide 143 1097. 0.130
3 Abiraterone 147 1038. 0.142
4 Carboplatin 78 1030. 0.0757
5 Cabazitaxel 144 962. 0.150
6 Docetaxel 122 922. 0.132
$`TP53- & AR-`
# A tibble: 6 x 4
trt progressions PT rate
<fct> <dbl> <dbl> <dbl>
1 Control 197 1454. 0.136
2 Enzalutamide 54 347. 0.156
3 Abiraterone 74 503. 0.147
4 Carboplatin 44 626. 0.0703
5 Cabazitaxel 76 585. 0.130
6 Docetaxel 51 398. 0.128
$`TP53+`
# A tibble: 6 x 4
trt progressions PT rate
<fct> <dbl> <dbl> <dbl>
1 Control 108 702. 0.154
2 Enzalutamide 65 595. 0.109
3 Abiraterone 54 381. 0.142
4 Carboplatin 27 319. 0.0846
5 Cabazitaxel 50 312. 0.160
6 Docetaxel 50 315. 0.159
$`DRD+`
# A tibble: 6 x 4
trt progressions PT rate
<fct> <dbl> <dbl> <dbl>
1 Control 65 470. 0.138
2 Enzalutamide 18 112. 0.161
3 Abiraterone 10 105. 0.0950
4 Carboplatin 24 269. 0.0893
5 Cabazitaxel 26 236. 0.110
6 Docetaxel 22 181. 0.122
$`TEfus+`
# A tibble: 6 x 4
trt progressions PT rate
<fct> <dbl> <dbl> <dbl>
1 Control 89 599. 0.148
2 Enzalutamide 48 348. 0.138
3 Abiraterone 45 254. 0.177
4 Carboplatin 25 297. 0.0843
5 Cabazitaxel 64 478. 0.134
6 Docetaxel 51 416. 0.123 
Kaplan-Meier results:
$all
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)
n events median 0.95LCL 0.95UCL
trt=Control 439 334 4.76 4.35 5.73
trt=Enzalutamide 166 143 5.90 5.17 7.19
trt=Abiraterone 181 147 5.33 4.43 6.37
trt=Carboplatin 89 78 9.00 6.19 13.45
trt=Cabazitaxel 164 144 4.74 3.88 5.73
trt=Docetaxel 158 122 5.18 4.56 6.54
$`TP53- & AR-`
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)
n events median 0.95LCL 0.95UCL
trt=Control 253 197 4.83 4.19 6.55
trt=Enzalutamide 58 54 5.78 3.66 7.94
trt=Abiraterone 85 74 5.26 3.83 6.58
trt=Carboplatin 52 44 10.12 5.65 16.18
trt=Cabazitaxel 91 76 5.73 5.20 7.01
trt=Docetaxel 70 51 4.70 3.88 6.93
$`TP53+`
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)
n events median 0.95LCL 0.95UCL
trt=Control 144 108 4.42 3.63 5.55
trt=Enzalutamide 83 65 6.86 5.19 9.23
trt=Abiraterone 68 54 5.23 3.86 7.35
trt=Carboplatin 29 27 9.00 6.23 17.01
trt=Cabazitaxel 55 50 4.28 3.17 6.18
trt=Docetaxel 55 50 5.26 3.61 6.85
$`DRD+`
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)
n events median 0.95LCL 0.95UCL
trt=Control 79 65 5.03 3.27 7.00
trt=Enzalutamide 19 18 4.16 2.22 12.39
trt=Abiraterone 19 10 4.96 4.20 NA
trt=Carboplatin 25 24 6.71 5.63 15.06
trt=Cabazitaxel 36 26 6.74 3.88 13.33
trt=Docetaxel 30 22 6.54 3.88 9.26
$`TEfus+`
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)
n events median 0.95LCL 0.95UCL
trt=Control 119 89 4.95 3.65 6.41
trt=Enzalutamide 53 48 5.46 4.82 9.40
trt=Abiraterone 51 45 3.48 2.60 5.54
trt=Carboplatin 28 25 7.04 5.49 17.01
trt=Cabazitaxel 77 64 5.18 3.88 6.33
trt=Docetaxel 68 51 5.26 4.56 8.30
